hicrep-package {hicrep} | R Documentation |
The pipelne is a two-step method. The first step is to smooth the Hi-C matrix, and the #' second step is to calculate the stratum-adjusted correlation coefficient (scc). The method also provides the estimation of asymptotic standard deviation of scc.
Package: hicrep
Type: Package
Version: 0.99.6
Date: 2017-2-5
License: GPL-2
LazyLoad: Yes
The main functions are prep
, get.scc
and
htrain
. The function prep
will take the
two replicates of N*(3+N) matrix format as input, and return
the vectorized, smoothed or unsmoothed (when smoothing neighborhood
size parameter h = 0) Hi-C data, which will subsequently used to
compute stratum-adjusted correlation coefficients (scc). The function
get.scc
computes scc and its asymptotic standard
deviation, and the function htrain
estimates optimal
smoothing neighborhood size from the input matrices.
Tao Yang Maintainer: Tao Yang <xadmyangt@gmail.com>
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. bioRxiv 101386; doi: https://doi.org/10.1101/101386.
data(HiCR1) data(HiCR2) #Estimate the optimial smoothing neighborhood size parameter h_hat <- htrain(HiCR1, HiCR2, 1000000, 5000000, 0:2) h_hat <- 0 processed <- prep(HiCR1, HiCR2, 1000000, h_hat, 5000000) scc.out <- get.scc(processed, 1000000, 5000000) scc.out$scc scc.out$std